Align NatB, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)
to candidate YP_426833.1 Rru_A1746 extracellular ligand-binding receptor
Query= TCDB::Q8YVY4 (441 letters) >NCBI__GCF_000013085.1:YP_426833.1 Length = 368 Score = 87.0 bits (214), Expect = 9e-22 Identities = 79/266 (29%), Positives = 116/266 (43%), Gaps = 30/266 (11%) Query: 51 SGGSGLKIGSLLPATGDLASIGQQMAAAVPLVVETVNACGGVNGQPVSLVAVDDQTDPKA 110 S + + +G P TG AS G+Q+A V+ +NA GGV G+ + L DD DPK Sbjct: 21 SAQADITVGVAGPMTGQYASFGEQLAKGAEQAVKDINAKGGVLGEKLVLKKGDDACDPKQ 80 Query: 111 GAAGMTKLATVDKVAGVVGSFASSVSTAAVSIAAQNKVLLISPGSTSPVFTEKAQKGDFN 170 A + DKV V G F S S A ++ + ++ ISP ST+P TE+ + F Sbjct: 81 AVAVANQFVN-DKVVFVAGHFCSGSSIPASAVYNEEGIVQISPASTNPKLTEQGFENVF- 138 Query: 171 GFWARTVPPDSYQGPALAEL--ANKKGFKRVSTIVINNDYGVGFEKAFVQAFEKLGG--- 225 RT D QGP + A+ G ++++ I YG G A K G Sbjct: 139 ----RTCGRDDQQGPTAGDFLKAHFPG-QKIAIIHDKTAYGKGLADETKSALNKAGVQEA 193 Query: 226 -----TVVNKNNPVRYDPKATTFETEAAAAFAGKPDAVLGVFYVETGSLLLKSAYQQGVA 280 T K+ Y T + E G LG ++ E G L+++ A +QG+ Sbjct: 194 LYEAITAGEKD----YSALVTKLKNE------GIKIIYLGGYHTEAG-LIIRQAKEQGL- 241 Query: 281 QGVQIMLTDGMKSDEFPAQVGKTADG 306 +I+ D + S EF + G DG Sbjct: 242 -DARIVSGDALVSSEFASIAGPAGDG 266 Lambda K H 0.312 0.130 0.367 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 372 Number of extensions: 19 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 441 Length of database: 368 Length adjustment: 31 Effective length of query: 410 Effective length of database: 337 Effective search space: 138170 Effective search space used: 138170 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory